Analysis of Overlapped and Noisy Hydrogen/Deuterium Exchange Mass Spectra

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1007/s13361-013-0727-5.Noisy and overlapped mass spectrometry data hinders the sequence coverage that can be obtained from Hydrogen Deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are reencountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regression for calculating the accurate deuterium content for mass envelopes of low signal or that contain significant overlap. The approach is demonstrated with a test data set of HIV Env gp140 wherein inclusion of the new analysis regime resulted in obtaining exchange data for 42 additional peptides, improving the sequence coverage by 11%. At the same time, the precision of deuterium uptake measurements was improved for nearly every peptide examined. The improved processing algorithms also provide an efficient method for deconvolution of bimodal mass envelopes and EX1 kinetic signatures. All these functions and visualization tools have been implemented in the new version of the freely available software, HX-Express v2

Attainment rate as a surrogate indicator of the intervertebral neutral zone length in lateral bending: An in vitro proof of concept study

Background Lumbar segmental instability is often considered to be a cause of chronic low back pain. However, defining its measurement has been largely limited to laboratory studies. These have characterised segmental stability as the intrinsic resistance of spine specimens to initial bending moments by quantifying the dynamic neutral zone. However these measurements have been impossible to obtain in vivo without invasive procedures, preventing the assessment of intervertebral stability in patients. Quantitative fluoroscopy (QF), measures the initial velocity of the attainment of intervertebral rotational motion in patients, which may to some extent be representative of the dynamic neutral zone. This study sought to explore the possible relationship between the dynamic neutral zone and intervertebral rotational attainment rate as measured with (QF) in an in vitro preparation. The purpose was to find out if further work into this concept is worth pursuing. Method This study used passive recumbent QF in a multi-segmental porcine model. This assessed the intrinsic intervertebral responses to a minimal coronal plane bending moment as measured with a digital force guage. Bending moments about each intervertebral joint were calculated and correlated with the rate at which global motion was attained at each intervertebral segment in the first 10° of global motion where the intervertebral joint was rotating. Results Unlike previous studies of single segment specimens, a neutral zone was found to exist during lateral bending. The initial attainment rates for left and right lateral flexion were comparable to previously published in vivo values for healthy controls. Substantial and highly significant levels of correlation between initial attainment rate and neutral zone were found for left (Rho = 0.75, P = 0.0002) and combined left-right bending (Rho = 0.72, P = 0.0001) and moderate ones for right alone (Rho = 0.55, P = 0.0012). Conclusions This study found good correlation between the initial intervertebral attainment rate and the dynamic neutral zone, thereby opening the possibility to detect segmental instability from clinical studies. However the results must be treated with caution. Further studies with multiple specimens and adding sagittal plane motion are warranted

The Photosynthetic Apparatus and Its Regulation in the Aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov

BACKGROUND: There is accumulating evidence that in some marine environments aerobic bacteriochlorophyll a-producing bacteria represent a significant part of the microbial population. The interaction of photosynthesis and carbon metabolism in these interesting bacteria is still largely unknown and requires further investigation in order to estimate their contribution to the marine carbon cycle. METHODOLOGY/PRINCIPAL FINDINGS: Here, we analyzed the structure, composition and regulation of the photosynthetic apparatus in the obligately aerobic marine gammaproteobacterium KT71(T). Photoheterotrophically grown cells were characterized by a poorly developed lamellar intracytoplasmic membrane system, a type 1 light-harvesting antenna complex and a photosynthetic reaction center associated with a tetraheme cytochrome c. The only photosynthetic pigments produced were bacteriochlorophyll a and spirilloxanthin. Under semiaerobic conditions KT71(T) cells expressing a photosynthetic apparatus showed a light-dependent increase of growth yield in the range of 1.3-2.5 fold. The expression level of the photosynthetic apparatus depended largely on the utilized substrate, the intermediary carbon metabolism and oxygen tension. In addition, pigment synthesis was strongly influenced by light, with blue light exerting the most significant effect, implicating that proteins containing a BLUF domain may be involved in regulation of the photosynthetic apparatus. Several phenotypic traits in KT71(T) could be identified that correlated with the assumed redox state of growing cells and thus could be used to monitor the cellular redox state under various incubation conditions. CONCLUSIONS/SIGNIFICANCE: In a hypothetical model that explains the regulation of the photosynthetic apparatus in strain KT71(T) we propose that the expression of photosynthesis genes depends on the cellular redox state and is maximal under conditions that allow a balanced membrane redox state. So far, bacteria capable of an obligately aerobic, photosynthetic metabolism constitute a unique phenotype within the class Gammaproteobacteria, so that it is justified to propose a new genus and species, Congregibacter litoralis gen. nov, sp. nov., represented by the type strain KT71(T) ( = DSM 17192(T) = NBRC 104960(T))

A Folding Pathway-Dependent Score to Recognize Membrane Proteins

While various approaches exist to study protein localization, it is still a challenge to predict where proteins localize. Here, we consider a mechanistic viewpoint for membrane localization. Taking into account the steps for the folding pathway of α-helical membrane proteins and relating biophysical parameters to each of these steps, we create a score capable of predicting the propensity for membrane localization and call it FP3mem. This score is driven from the principal component analysis (PCA) of the biophysical parameters related to membrane localization. FP3mem allows us to rationalize the colocalization of a number of channel proteins with the Cav1.2 channel by their fewer propensities for membrane localization